Contacts of the helix formed by residues 610 - 623 (chain K) in PDB entry 6QX2
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 610 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13J ASN* 5.4 0.4 - - - +
15J THR* 5.1 0.9 + - - -
608K LEU* 3.9 3.3 - - - +
609K GLU* 1.3 77.3 - - + +
611K ALA* 1.3 57.7 + - - +
612K ILE* 3.1 26.2 + - - +
613K GLU* 3.4 34.2 + - + +
614K ALA* 3.0 27.5 + - - +
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Residues in contact with ALA 611 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525K TYR* 3.0 9.1 + - - +
529K ARG* 3.2 35.2 - - - +
608K LEU* 4.0 12.5 - - + +
609K GLU 4.0 3.6 + - - -
610K ASP* 1.3 70.6 + - - +
612K ILE* 1.3 61.0 + - + +
614K ALA 3.5 0.2 + - - -
615K ASP* 2.9 35.0 + - - +
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Residues in contact with ILE 612 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610K ASP* 3.1 11.3 + - - +
611K ALA* 1.3 78.4 - - + +
613K GLU* 1.3 62.4 + - - +
615K ASP* 3.3 10.7 + - - +
616K GLN* 3.2 44.5 + - + +
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Residues in contact with GLU 613 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J THR* 4.3 21.0 - - + +
19J ARG* 5.6 4.1 + - - +
610K ASP* 3.4 33.5 + - + +
612K ILE* 1.3 75.3 - - - +
614K ALA* 1.3 59.9 + - - +
616K GLN* 3.5 15.6 + - + +
617K THR* 3.0 38.6 + - - +
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Residues in contact with ALA 614 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J ILE* 4.6 7.2 - - + -
15J THR* 4.0 14.5 + - - +
525K TYR* 3.4 29.2 - - + +
608K LEU* 3.8 11.0 - - + -
610K ASP 3.0 17.9 + - - +
611K ALA 3.6 0.4 - - - +
613K GLU* 1.3 74.0 - - - +
615K ASP* 1.3 63.8 + - - +
617K THR* 3.1 3.5 + - - -
618K PHE* 3.0 35.7 + - + -
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Residues in contact with ASP 615 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525K TYR* 3.0 14.2 + - - -
526K ARG* 3.1 37.0 + - - +
529K ARG* 4.2 10.5 + - - -
611K ALA* 2.9 25.9 + - - +
612K ILE* 3.6 11.8 - - - +
614K ALA* 1.3 74.8 - - - +
616K GLN* 1.3 61.6 + - + +
619K GLU* 3.3 23.8 + - - +
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Residues in contact with GLN 616 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612K ILE* 3.2 33.1 + - + +
613K GLU* 3.7 18.2 - - - +
614K ALA 3.2 0.2 - - - -
615K ASP* 1.3 76.3 - - + +
617K THR* 1.3 59.0 + - - +
619K GLU* 3.5 13.6 + - - +
620K MET* 3.0 31.1 + - - +
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Residues in contact with THR 617 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J THR* 4.0 19.8 - - - +
18J MET* 4.1 14.4 - - + -
19J ARG* 2.9 41.1 + - + +
613K GLU* 3.0 20.0 + - - +
614K ALA 3.1 4.5 + - - -
616K GLN* 1.3 74.0 - - - +
618K PHE* 1.3 61.4 + - + +
620K MET* 3.4 3.8 + - - +
621K LEU* 3.0 54.4 + - + +
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Residues in contact with PHE 618 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J ILE* 3.7 25.8 - - + -
15J THR* 6.1 1.1 - - - -
18J MET* 3.7 30.3 - - + -
465K GLU* 3.9 5.7 - - - +
521K LEU* 3.7 3.8 - - + -
522K THR* 3.2 48.7 - - + -
525K TYR* 3.6 42.4 - + + -
526K ARG* 3.8 18.6 - - - +
614K ALA* 3.0 31.6 + - + +
617K THR* 1.3 73.4 - - + +
619K GLU* 1.3 58.9 + - - +
621K LEU* 5.0 0.7 - - - -
622K MET* 2.8 39.1 + - + +
623K GLY 3.5 0.7 + - - -
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Residues in contact with GLU 619 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465K GLU* 3.4 17.8 + - - +
526K ARG* 4.4 1.6 - - - +
615K ASP 3.3 19.3 + - - +
616K GLN* 3.7 13.2 - - - +
618K PHE* 1.3 77.4 - - - +
620K MET* 1.3 57.7 + - - +
623K GLY* 3.1 27.1 + - - +
625K VAL* 5.5 3.3 + - - +
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Residues in contact with MET 620 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J ARG* 3.5 32.1 - - - +
616K GLN 3.0 16.9 + - - +
617K THR* 3.8 2.9 - - - +
618K PHE 3.2 0.2 - - - -
619K GLU* 1.3 76.4 - - - +
621K LEU* 1.3 76.1 + - + +
625K VAL 4.4 3.6 - - - +
628K ASN* 3.9 32.3 - - + +
629K ARG* 3.5 27.1 + - - +
632K PHE* 3.7 37.9 - - + -
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Residues in contact with LEU 621 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18J MET* 3.7 46.0 - - + +
19J ARG* 4.1 4.9 - - + +
22J PHE* 3.6 27.4 - - + -
617K THR* 3.0 29.4 + - + +
620K MET* 1.3 89.9 - - + +
622K MET* 1.3 69.7 + - + +
629K ARG* 2.8 32.8 + - - +
632K PHE* 3.3 38.1 - - + -
16O C 4.9 1.4 + - - -
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Residues in contact with MET 622 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J MET* 3.9 17.5 - - + -
22J PHE* 3.9 18.6 - - + -
463K ASN* 3.1 31.5 + - - +
465K GLU* 3.2 25.3 - - + +
466K LYS* 3.4 5.8 - - - +
518K THR* 3.6 18.4 - - - +
519K LEU* 3.7 26.5 - - + -
522K THR* 3.2 28.5 - - + +
618K PHE* 2.8 20.2 + - + +
621K LEU* 1.3 83.4 - - + +
623K GLY* 1.3 65.1 + - - +
629K ARG* 4.0 0.9 - - - +
16O C 4.2 7.2 - - - +
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Residues in contact with GLY 623 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465K GLU* 3.7 13.7 - - - -
466K LYS* 3.4 5.4 - - - -
618K PHE 3.5 1.4 + - - -
619K GLU* 3.1 25.8 + - - -
621K LEU 3.6 0.6 - - - -
622K MET* 1.3 79.4 - - - +
624K ASP* 1.3 59.6 + - - -
625K VAL 3.3 3.6 - - - -
629K ARG* 2.7 27.7 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il